When I roam about the directory structure, it appears that all files may
actually still be there, but the structure is now that of several nested
levels of archive, like it stuffed one inside the other. There are
actually three nested "archives" directories, and the inner two are rather
huge.

This is a wintel box. I'm starting to be suspicious that there may be some
finite limit in the number of directories any particular directory can
contain. If that is so, and if greenstone actually wants to build just one
archives directory and put everything in there, then it's beginning to feel
like greenstone has some practical limit in collection size -- don't recall
reading anything about that elsewhere.